The flow-sorted human chromosome is an ideal DNA source for genome analysis research, particularly gene mapping and construction of cosmid library. For gene mapping, 50,000 chromosomes each were sorted on a membrane filter and hybridized with a radio-labeled gene probe. Using this Spot Blot Hybridization method in combination with FISH, we have mapped more than 30 new genes including 6 neuron-specific ones. For construction of a chromosome-specific cosmid library, nearly 10 million chromosomes were flow-sorted. The chromosome 21-specific cosmid library consisting of 33,000 clones and the 22pter-q11 region-specific library consisting of 9,200 clones were established. Grouping of cosmid clones from the library using high density replica filters and YAC DNAs to make cosmid contigs within specific regions is under way.